From jalview-announce at jalview.org  Fri Aug 11 10:33:49 2006
From: jalview-announce at jalview.org (jalview-announce@jalview.org)
Date: Fri Aug 11 10:32:17 2006
Subject: [Jalview-announce] Jalview 2.1
Message-ID: <44DC4EFD.3000603@compbio.dundee.ac.uk>

Hello there Jalview Users,

This is an pre-release message just to let you know that the next 
release of Jalview should be available within the next 2 weeks.

We are nearing the end of coding time, and will spend some time updating 
all the documentation before the new release.

The new features in the Jalview 2.1 will be:

   * MAFFT Multiple Alignment in default Web Service list
   * DAS Feature fetching
   * Hidden Sequences, Hidden Columns
   * Annotation / Features export
   * GFF file reading / writing
   * Add sequences to existing alignment
   * Wrap alignment as a preference
   * Recently opened files / URL lists
   * Associate structures with sequences from local PDB files
   * Applet can launch the  full application
   * Applet has transparency for features
   * Applet has user defined colours

Issues resolved:
  * Redundancy Panel reinstalled in the Applet version
  * Monospaced font - EPS / rescaling bug fixed
  * Annotation files with sequence references bug fixed


Bye for now,

Andrew


From jalview-announce at jalview.org  Tue Aug 22 17:45:28 2006
From: jalview-announce at jalview.org (jalview-announce@jalview.org)
Date: Tue Aug 22 17:43:44 2006
Subject: [Jalview-announce] Jalview 2.1 Available
Message-ID: <44EB34A8.7000800@compbio.dundee.ac.uk>

Hello there Jalview Users,

We are pleased to announce that Jalview 2.1 is now available to download 
from http://www.jalview.org

The new features in the Jalview 2.1 are:

  * MAFFT Multiple Alignment in default Web Service list
  * DAS Feature fetching
  * Hidden Sequences, Hidden Columns
  * Annotation / Features export
  * GFF file reading / writing
  * Add sequences to existing alignment
  * Wrap alignment as a preference
  * Recently opened files / URL lists
  * Associate structures with sequences from local PDB files
  * Applet can launch the  full application
  * Applet has transparency for features
  * Applet has user defined colours
  * Applet can be fed sequences as parameters

Issues resolved:
 * Redundancy Panel reinstalled in the Applet version
 * Monospaced font - EPS / rescaling bug fixed
 * Annotation files with sequence references bug fixed


Let us know what you think of the updates!!






From jalview-announce at jalview.org  Wed Aug 23 09:30:55 2006
From: jalview-announce at jalview.org (jalview-announce@jalview.org)
Date: Wed Aug 23 09:29:12 2006
Subject: [Jalview-announce] Jalview 2.1 Applet
Message-ID: <44EC123F.9080104@compbio.dundee.ac.uk>

Hello all,

This is related to those installing the Jalview 2.1 applet.

 I would like to ask if you would consider using the parameter

<param name="APPLICATION_URL" 
value="http://www.jalview.org/services/launchApp">

If this parameter is supplied, there will be an extra menu item in the 
File menu, labelled "View in Full Application". If this is selected, a 
servlet is called which generates a JNLP page using the file name (and 
features file and annotations file if available) so the original data 
will be visible in the full application.

However, this will only work if the user already has Java installed on 
their machine, if not they will get the XML page returned and not know 
what to do with it. It also requires the user to allow popups, it seems 
most modern browsers are set to block popups by default. These are the 
common problems we can foresee with this new feature.

Try it out with the example applets on 
http://www.jalview.org/examples/applets.html.

If you find this is useful, or the functionality needs extending, let us 
know!


Andrew


From jalview-announce at jalview.org  Tue Sep 12 13:30:48 2006
From: jalview-announce at jalview.org (jalview-announce@jalview.org)
Date: Tue Sep 12 13:28:30 2006
Subject: [Jalview-announce] Jalview 2.1.1
Message-ID: <4506A878.2000808@compbio.dundee.ac.uk>

Hello all,

Theres a new Jalview release, 2.1.1, available for download now which 
addresses a number of bug reports we've had other the past couple of 
weeks. As they affect data input (if using annotation files with 
sequence references) and image output we deemed it necessary to get this 
bug fix release out as soon as possible.

    * Image output - rightmost residues are rendered if sequence id
      panel has been resized or /start-end suffix is omitted.
    * Image output - all offscreen group boundaries are rendered
    * Annotation files with sequence references - all elements in file
      are relative to sequence position
    * Mac Applet users can use Alt key for group editing

A simple new feature added is the ability to copy the consensus sequence 
to clipboard.



Thanks again for using Jalview!